De Novo Non-Canonical Nanopore Basecalling Enables Private Communication using Heavily-modified DNA Data at Single-Molecule Level
Year: 2025
Type: article
Abstract: This repostry contains the sequencing pod5 files from 5hmC-modified 6-mer QC sequences, Bacterial Genome DNA (gDNA) sequences, DNA Storage sequences for training the 5hmC DeepSME basecaller and conducting the DNA storage decoding experiments. File Description 5hmc_pod5_for_training_reinforced_deepsme.zip pod5 file for training the 5hmC reinforced DeepSME, reference FASTA can be retrieved from NCBI ( Pseudomonas_aeruginosa_PAO1 (https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000006765.1/ ), Aeromonas_hydrophila_BJ054 (https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_046708825.1/ ), and Vibrio_cholera_E1 (https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_026013235.1/ )) 5hmc_pod5_for_training_6mer_qc_deepsme.zip pod5 file for training the 5hmC 6-mer QC DeepSME, reference FASTA can be retrieved from https://github.com/sparkcyf/DeepSME 5hmc_pod5_sustech_seqs.pod5 pod5 file for 5hmC DNA Storage sequences, reference FASTA and decode scripts can be retrieved from https://github.com/sparkcyf/DeepSME_DNA_Storage_Decode_scripts_DeepSME/ deepsme_dna_5hmc_r9.4.1_e8_sup_dorado.tar.gz 5hmC reinforced DeepSME, Dorado (https://github.com/nanoporetech/dorado ) Format deepsme_dna_5hmc_r9.4.1_e8_sup_bonito.tar.gz 5hmC reinforced DeepSME, Bonito (https://github.com/nanoporetech/bonito ) Format
Author: Fan, Qingyuan
Institution: Southern University of Science and Technology
Language: English
Topic: DNA and Biological Computing
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W6930233635
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